March 13, 2012

Auxiliary TreeMix scripts

Joe Pickrell has put up a useful Python script for TreeMix in the software page. It takes in PLINK-formatted input and transforms it into TreeMix-formatted input. You only need to specify a PLINK cluster file to indicate the correspondence between individuals and populations.

I was planning to release my own R script that does the same, and which I've used to produce this, but it is now redundant.

But since some people might want to try TreeMix with ADMIXTURE components, I am releasing my script that takes ADMIXTURE output and produces TreeMix output.

2 comments:

Could you please specify the structure of cluster file? The cluster file I have (plink output) is somehow not working. I have bed, bim, fam, ped and cluster file for my data but the python script supplied along with treemix is probably unable to recognize it. Requesting tips and pointers on that. Thanks

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